⚠

NOTICE! This is a static HTML version of a legacy Fiji BugZilla bug.

The Fiji project now uses GitHub Issues for issue tracking.

Please file all new issues there.

Bug 814 - transposons on script editor
transposons on script editor
Status: NEEDSINFO
Product: Fiji
Classification: Unclassified
Component: Plugins
unspecified
PC Linux
: P4 normal
Assigned To: ImageJ Bugs Mailing List
Depends on:
Blocks:
 
Reported: 2014-06-25 07:01 CDT by Aryeh Weiss
Modified: 2014-07-25 07:35 CDT
2 users (show)

See Also:

Attachments
Essential frames of the transposons (2.62 MB, image/gif)
2014-07-23 17:24 CDT, Johannes Schindelin

Description Aryeh Weiss 2014-06-25 07:01:01 CDT 
The script editor seems to copy strings and put them in random places. This typically occurs whle developing a macro. I find that some string which had been previously cut and paste now appears in 3-4  places, often inserted in the middle of some other line.
When that happens, the macro crashes, which is ok. The real problem is when a valid line of code gets put someplace where it is not invalid. Then the code may run, with some very puzzling results.
Finally, sometimes it does not invalidate the code, and then you can accumulate "junk" lines.

SImilar behavior can be found in the genome -- maybe Fiji is evolving into something that lives...

Information about your version of Java:

  os.arch => amd64
  os.name => Linux
  os.version => 3.11.10-11-desktop
  java.version => 1.6.0_24
  java.vendor => Sun Microsystems Inc.
  java.runtime.name => Java(TM) SE Runtime Environment
  java.runtime.version => 1.6.0_24-b07
  java.vm.name => Java HotSpot(TM) 64-Bit Server VM
  java.vm.version => 19.1-b02
  java.vm.vendor => Sun Microsystems Inc.
  java.vm.info => mixed mode
  java.awt.graphicsenv => sun.awt.X11GraphicsEnvironment
  java.specification.name => Java Platform API Specification
  java.specification.version => 1.6
  sun.cpu.endian => little
  sun.desktop => null
  file.separator => /

The up-to-date check says: REMIND_LATER

Information relevant to JAVA_HOME related problems:

  JAVA_HOME is set to: /home/victoria/Desktop/Fiji.app/java/linux-amd64/jdk1.6.0_24//jre
  imagej.dir => /home/victoria/Desktop/Fiji.app

Information about the version of each plugin:

Activated update sites:
ImageJ: http://update.imagej.net/ (last check:20140623232553)
Fiji: http://fiji.sc/update/ (last check:20140624012555)
3D ImageJ Suite: http://sites.imagej.net/Tboudier/ (last check:20140604090506)
Bio-Formats: http://sites.imagej.net/Bio-Formats/ (last check:20140624184012)
BioVoxxel: http://sites.imagej.net/BioVoxxel/ (last check:20140519212603)
Cookbook: http://sites.imagej.net/Cookbook/ (last check:20131221011857)
CMCI-EMBL: http://sites.imagej.net/Miura/ (last check:20140617140816)
CMP-BIA tools: http://sites.imagej.net/CMP-BIA/ (last check:20140423173817)
FFMPEG: http://fiji.sc/~schindelin/ffmpeg-plugins/ (last check:20130606182449)
IBMP-CNRS: http://www-ibmp.u-strasbg.fr/fijiupdates/ (last check:20140526174644)
IMCF Uni Basel: http://sites.imagej.net/UniBas-IMCF/ (last check:20140521190037)
LOCI: http://sites.imagej.net/LOCI/ (last check:20140401215514)
MOSAIC ToolSuite: http://mosaic.mpi-cbg.de/Downloads/update/Fiji/MosaicToolsuite/ (last check:20140624175404)
ScientiFig: http://sites.imagej.net/Aigouy/ (last check:20140516145525)

Files not up-to-date:
  de46805b (MODIFIED) 20140625101452 jars/ij-1.49b.jar
  d84cc2bb (LOCAL_ONLY) 20100922224634 plugins/Morphology/Add_Borders.class
  5cccefae (LOCAL_ONLY) 20100913105427 plugins/Morphology/AnnularClosing.txt
  763870ef (LOCAL_ONLY) 20100913105434 plugins/Morphology/AnnularDilation.txt
  5d777e5e (LOCAL_ONLY) 20100928180029 plugins/Morphology/BinaryConditionalDilate_.class
  6cfae168 (LOCAL_ONLY) 20060525212651 plugins/Morphology/BinaryConditionalErode_.class
  877be8e6 (LOCAL_ONLY) 20060525212957 plugins/Morphology/BinaryConnectivity_.class
  ebe4d9b0 (LOCAL_ONLY) 20111110115448 plugins/Morphology/BinaryDilateNoMerge4_.class
  65b35fcd (LOCAL_ONLY) 20111109185612 plugins/Morphology/BinaryDilateNoMerge8_.class
  da5dc033 (LOCAL_ONLY) 20081019162449 plugins/Morphology/BinaryDilateTest.txt
  fe9208a2 (LOCAL_ONLY) 20060525213011 plugins/Morphology/BinaryDilate_.class
  9f2b4ef9 (LOCAL_ONLY) 20081019162917 plugins/Morphology/BinaryErodeTest.txt
  b38e2aa0 (LOCAL_ONLY) 20060525213102 plugins/Morphology/BinaryErode_.class
  3f39caaf (LOCAL_ONLY) 20060525121716 plugins/Morphology/BinaryFilterReconstruct.txt
  76eb6799 (LOCAL_ONLY) 20090525213222 plugins/Morphology/BinaryFilterReconstruct_.class
  6a2c8b7a (LOCAL_ONLY) 20111109184430 plugins/Morphology/BinaryGeodesicDilateNoMerge8_.class
  14c67860 (LOCAL_ONLY) 20080602111843 plugins/Morphology/BinaryHitOrMiss_.class
  33b507c2 (LOCAL_ONLY) 20100418172848 plugins/Morphology/BinaryKillBorders_.class
  4204c1c6 (LOCAL_ONLY) 20101206112939 plugins/Morphology/BinaryLabel8_.class
  d3c84f8c (LOCAL_ONLY) 20070712132239 plugins/Morphology/BinaryLabelMacro.txt
  59e1afe9 (LOCAL_ONLY) 20100508105308 plugins/Morphology/BinaryLabel_.class
  36e4a042 (LOCAL_ONLY) 20060525121717 plugins/Morphology/BinaryPrune.txt
  c8c66f92 (LOCAL_ONLY) 20090526185400 plugins/Morphology/BinaryReconstruct_.class
  3ff298c7 (LOCAL_ONLY) 20060525213501 plugins/Morphology/BinaryThick2_.class
  b73f68f4 (LOCAL_ONLY) 20060525213450 plugins/Morphology/BinaryThick_.class
  2c4c813e (LOCAL_ONLY) 20060525213520 plugins/Morphology/BinaryThin2_.class
  d8a5d664 (LOCAL_ONLY) 20060525213512 plugins/Morphology/BinaryThin_.class
  3e83cc61 (LOCAL_ONLY) 20060525121717 plugins/Morphology/Boundary4.txt
  9d64440e (LOCAL_ONLY) 20060525121717 plugins/Morphology/Boundary8_.txt
  e9fc745d (LOCAL_ONLY) 20090602173322 plugins/Morphology/Catalogue_Particles.txt
  4d0095a2 (LOCAL_ONLY) 20070607110847 plugins/Morphology/Classify_Particles.class
  f53a898e (LOCAL_ONLY) 20090511103446 plugins/Morphology/CloseByReconstructionTopHat.txt
  2c7f38f5 (LOCAL_ONLY) 20101005113839 plugins/Morphology/CloseByReconstruction_.txt
  1c33105a (LOCAL_ONLY) 20060525121717 plugins/Morphology/ConvexHull1.txt
  7cb69fdf (LOCAL_ONLY) 20060525121717 plugins/Morphology/ConvexHull2.txt
  b19cb415 (LOCAL_ONLY) 20060525121717 plugins/Morphology/ConvexHull3.txt
  bd22187f (LOCAL_ONLY) 20060525121717 plugins/Morphology/Corners.txt
  55c709bf (LOCAL_ONLY) 20061116122256 plugins/Morphology/Correlate_Results.class
  d463ee86 (LOCAL_ONLY) 20081019173010 plugins/Morphology/Delete_ZeroArea.txt
  8df2eb76 (LOCAL_ONLY) 20060525121717 plugins/Morphology/Diagonal8to4.txt
  61193e21 (LOCAL_ONLY) 20100929135932 plugins/Morphology/Domes_.class
  e428a0f5 (LOCAL_ONLY) 20060525121717 plugins/Morphology/Domes_stack.txt
  1be944ae (LOCAL_ONLY) 20090506102436 plugins/Morphology/DoubleWaterfall.txt
  925d3d8c (LOCAL_ONLY) 20111208121209 plugins/Morphology/DrawBoundingBox.txt
  63c4cd27 (LOCAL_ONLY) 20111208121157 plugins/Morphology/DrawBoundingCircle.txt
  b97f945a (LOCAL_ONLY) 20111208121141 plugins/Morphology/DrawConvexHulls.txt
  2adcfe94 (LOCAL_ONLY) 20111208121226 plugins/Morphology/DrawFeret&Breadth.txt
  b60f4365 (LOCAL_ONLY) 20111208121235 plugins/Morphology/DrawMinR&MaxR.txt
  288ace7a (LOCAL_ONLY) 20100805144115 plugins/Morphology/EDM_16bits.txt
  71d10273 (LOCAL_ONLY) 20081019180232 plugins/Morphology/Euler.txt
  63757672 (LOCAL_ONLY) 20090511103446 plugins/Morphology/Extended_Maxima.txt
  285e4c16 (LOCAL_ONLY) 20090511103446 plugins/Morphology/Extended_Minima.txt
  2b80b381 (LOCAL_ONLY) 20100418195425 plugins/Morphology/FillHolesReconstruct.txt
  205b6052 (LOCAL_ONLY) 20060525150101 plugins/Morphology/Fill_Border_Holes.txt
  54d7ef21 (LOCAL_ONLY) 20090506102436 plugins/Morphology/Fill_Greyscale_Holes.txt
  75041650 (LOCAL_ONLY) 20101001153722 plugins/Morphology/GreyBlackTopHatByReconstruction_.txt
  6f716dcc (LOCAL_ONLY) 20101001153322 plugins/Morphology/GreyWhiteTopHatByReconstruction_.txt
  579b5383 (LOCAL_ONLY) 20090504162458 plugins/Morphology/GreyscaleCentreFilter.txt
  c4267b67 (LOCAL_ONLY) 20060525213602 plugins/Morphology/GreyscaleDilate_.class
  965f297a (LOCAL_ONLY) 20060525213612 plugins/Morphology/GreyscaleErode_.class
  0a50379d (LOCAL_ONLY) 20100920142950 plugins/Morphology/GreyscaleKillBorders.txt
  d3047959 (LOCAL_ONLY) 20090503202435 plugins/Morphology/GreyscaleProperAutomedian.txt
  b4d94111 (LOCAL_ONLY) 20090504142819 plugins/Morphology/GreyscaleProperClose.txt
  44d81a95 (LOCAL_ONLY) 20090504142959 plugins/Morphology/GreyscaleProperOpen.txt
  9aadbae0 (LOCAL_ONLY) 20090526185731 plugins/Morphology/GreyscaleReconstruct_.class
  4d7e6035 (LOCAL_ONLY) 20100908164402 plugins/Morphology/GreyscaleTopHat.txt
  cb2dc22a (LOCAL_ONLY) 20100908164825 plugins/Morphology/GreyscaleWell.txt
  282495a6 (LOCAL_ONLY) 20060525121717 plugins/Morphology/H-break.txt
  a73d2279 (LOCAL_ONLY) 20090511150552 plugins/Morphology/HMaxima_Transform.txt
  f1c1b630 (LOCAL_ONLY) 20090527112132 plugins/Morphology/HMinima_Transform.txt
  af3183b2 (LOCAL_ONLY) 20080605142624 plugins/Morphology/Hole_Counter.txt
  930ee9e1 (LOCAL_ONLY) 20090527191615 plugins/Morphology/HomotopicMarking.txt
  3429c4f3 (LOCAL_ONLY) 20060525121717 plugins/Morphology/Hysteresis.txt
  2511df4c (LOCAL_ONLY) 20090513123655 plugins/Morphology/Impose_Minimum.txt
  6be72748 (LOCAL_ONLY) 20060525121717 plugins/Morphology/Influence_Zones.txt
  5859277c (LOCAL_ONLY) 20060525121717 plugins/Morphology/KeepLargestParticle.txt
  559e475f (LOCAL_ONLY) 20080522002500 plugins/Morphology/KeepLargestParticlePixels_.txt
  4605ad0a (LOCAL_ONLY) 20080605164601 plugins/Morphology/KeepParticlesInRange.txt
  b46b2695 (LOCAL_ONLY) 20110415171003 plugins/Morphology/Lines8_.class
  43259a0b (LOCAL_ONLY) 20090519141519 plugins/Morphology/LocalMaxima.txt
  c0207001 (LOCAL_ONLY) 20090519142405 plugins/Morphology/LocalMinMax.txt
  b2139bd8 (LOCAL_ONLY) 20090519141443 plugins/Morphology/LocalMinima.txt
  05f0502d (LOCAL_ONLY) 20060525121717 plugins/Morphology/MCentroids.txt
  b3ea5e05 (LOCAL_ONLY) 20101007155910 plugins/Morphology/MinimaDynamic.txt
  57e4bbaa (LOCAL_ONLY) 20060525121717 plugins/Morphology/Morphological2Derivative1.txt
  35b51e7e (LOCAL_ONLY) 20060525121717 plugins/Morphology/Morphological2Derivative2.txt
  ef809632 (LOCAL_ONLY) 20060525121717 plugins/Morphology/Morphological2Derivative3.txt
  73902be6 (LOCAL_ONLY) 20100908164213 plugins/Morphology/MorphologicalContrastTopHat.txt
  86d43a13 (LOCAL_ONLY) 20100906152436 plugins/Morphology/MorphologicalExternalGradient.txt
  66d657f2 (LOCAL_ONLY) 20100908193708 plugins/Morphology/MorphologicalGradient3.txt
  2cd67873 (LOCAL_ONLY) 20100906152436 plugins/Morphology/MorphologicalGradientBeucher.txt
  b141cc35 (LOCAL_ONLY) 20100906152436 plugins/Morphology/MorphologicalInternalGradient.txt
  babf8d91 (LOCAL_ONLY) 20060525121717 plugins/Morphology/MorphologicalSharpGradient.txt
  7e05ec43 (LOCAL_ONLY) 20060525121717 plugins/Morphology/MorphologicalSmoothing1.txt
  df30c851 (LOCAL_ONLY) 20060525121717 plugins/Morphology/MorphologicalSmoothing2.txt
  b4232d82 (LOCAL_ONLY) 20100913105525 plugins/Morphology/Morphological_Clustering.txt
  c4024220 (LOCAL_ONLY) 20100923004422 plugins/Morphology/Morphological_PCA.txt
  44b58573 (LOCAL_ONLY) 20101005111848 plugins/Morphology/Morphological_SelfDualCentre.txt
  d20caeeb (LOCAL_ONLY) 20101005173722 plugins/Morphology/Morphological_contrast.txt
  c40dcb5d (LOCAL_ONLY) 20100908164252 plugins/Morphology/MultiscaleGradient.txt
  7fa60ae6 (LOCAL_ONLY) 20110425191913 plugins/Morphology/NumberParticles8_.txt
  cd6cf4de (LOCAL_ONLY) 20090511103446 plugins/Morphology/OpenByReconstructionTopHat.txt
  5f844fa9 (LOCAL_ONLY) 20101005113855 plugins/Morphology/OpenByReconstruction_.txt
  8fdf1b15 (LOCAL_ONLY) 20080522001817 plugins/Morphology/Parameter_Matrix.txt
  65c22a1e (LOCAL_ONLY) 20080530004339 plugins/Morphology/ParticleHoleArea.txt
  9a713d79 (LOCAL_ONLY) 20080530004456 plugins/Morphology/ParticleHoleNumber.txt
  9c0a7763 (LOCAL_ONLY) 20080530004151 plugins/Morphology/Particle_Data_Map.txt
  85b99ff0 (LOCAL_ONLY) 20100914160815 plugins/Morphology/Particles4_.class
  583118b2 (LOCAL_ONLY) 20100914160807 plugins/Morphology/Particles8_.class
  ac25812c (LOCAL_ONLY) 20080521235826 plugins/Morphology/Plot_BivariateGraphs.txt
  e8ea53cb (LOCAL_ONLY) 20080606134751 plugins/Morphology/Plot_Histograms.txt
  ce077644 (LOCAL_ONLY) 20060525121717 plugins/Morphology/Prune1.txt
  c4126534 (LOCAL_ONLY) 20060525121717 plugins/Morphology/PruneAll.txt
  916ac5a4 (LOCAL_ONLY) 20090511103446 plugins/Morphology/RegionalMinMax.txt
  3dcf6fa2 (LOCAL_ONLY) 20090511103446 plugins/Morphology/Regional_Maxima.txt
  bc61499e (LOCAL_ONLY) 20101001123926 plugins/Morphology/Regional_Minima.txt
  358d5270 (LOCAL_ONLY) 20100923005811 plugins/Morphology/SelfComplementaryTopHat.txt
  36e7e0b4 (LOCAL_ONLY) 20101005104120 plugins/Morphology/SelfDualReconstruction_.txt
  64886ac9 (LOCAL_ONLY) 20060525121717 plugins/Morphology/Skeleton1.txt
  64fa451e (LOCAL_ONLY) 20060525121717 plugins/Morphology/Skeleton2.txt
  809a6770 (LOCAL_ONLY) 20060525121717 plugins/Morphology/Skeleton3.txt
  16447730 (LOCAL_ONLY) 20090511141301 plugins/Morphology/Skeleton4.txt
  b2242712 (LOCAL_ONLY) 20100922222400 plugins/Morphology/SkeletonFiltering.txt
  5d0400a0 (LOCAL_ONLY) 20080521235352 plugins/Morphology/Summarize_Results.txt
  ab0b29c3 (LOCAL_ONLY) 20080603131017 plugins/Morphology/Thin_Results_Table.txt
  090f96c1 (LOCAL_ONLY) 20100621110217 plugins/Morphology/UnbiasedCounting.txt
  fecf6a46 (LOCAL_ONLY) 20080605141015 plugins/Morphology/UnbiasedParticleArea.txt
  19a9433c (LOCAL_ONLY) 20090330100641 plugins/Morphology/Viscous_Geodesic_Reconstruction.txt
Comment 1 Johannes Schindelin 2014-06-25 09:44:41 CDT 
This is worrisome, in particular because I never encountered that bug myself, so I have no idea how to fix it. Yet.

Could I ask you to provide a little bit more information? Do you use Ctrl+C/Ctrl+V to copy/paste, or the mouse buttons, or the Edit menu?

Maybe the best way would be to look over your shoulder while you are doing this. Short of flying over to your place (which I would *love* to do, BTW), may I ask you to use Fiji's File>Make Screencast (it uses VLC; if you have not installed that program yet, the Make Screencast script should give you helpful instructions where to download an installer, although on Linux you probably know how to install VLC via apt-get anyway). This will allow you to record a movie of your screen while you write a simple macro (and hopefully the bug will occur pretty soon). I would be delighted to watch that movie after you uploaded it via Help>Upload Sample Image.
Comment 2 Aryeh Weiss 2014-06-25 13:14:54 CDT 
I noticed it with the ^C and ^Y, for sure. 
I cannot say whether it also occurred with copy from the pull down menu.

I will do a screen-cast  next week, when I am in that lab.
It is possible that if the program knows that I am looking, it may not act up...
Comment 3 Johannes Schindelin 2014-06-25 13:44:51 CDT 
> I will do a screen-cast  next week, when I am in that lab.

Thank you!

> It is possible that if the program knows that I am looking, it may not act up...

Ah, that would be quantum physics in addition to genetics, no?

In any case, I would *love* to identify those P-sites and cross them out.

:-)
Comment 4 Aryeh Weiss 2014-07-09 02:52:22 CDT 
I uploaded a screencast called screencast140629.ogv
A "transposon" was discovered at approx 22 minutes into the screencast.
There is much "needless" activity prior to this which was done because I was explaining many things to a student.

I can add that on my OSX system, I have discovered text inserted from the system clipboard that did not come from Fiji, but rather from other programs that were open at the same time.
Comment 5 Aryeh Weiss 2014-07-09 11:54:25 CDT 
On my OSX system, when I started the script editor, and opened a python script,
I found a spurious line a the top of the script. This line was a URL, which happened to the be last item which I had cut and pasted in a different program (Firefox). Whet is new here is that this was at the very beginning of the Fiji session, and I had just loaded the script, but I did no cut and paste operations.

I suspect that the script editor is pasting stuff from the system clipboard when this is not expected.
Comment 6 Johannes Schindelin 2014-07-23 17:24:49 CDT 
Created attachment 184
Essential frames of the transposons
Comment 7 Johannes Schindelin 2014-07-23 17:28:04 CDT 
Hmm. I tried to reproduce the issue, but was unable to.

Is it possible that your mouse has a really worn-out middle mouse button? Sometimes the mouse wheel serves as middle mouse button, too, so if it is quite jiggery, it is possible that it gets "clicked". This is interpreted by Linux' window manager as a paste event.

Another idea I have is that maybe the Alt key gets sticky. You can move the selection (or if nothing is selected, the current line) by using Alt+cursor movement.

But the fact that it happens at offset 19:40 (slice 4 in the animated GIF I attached) just after a wild scroll orgy and the fact that the cursor is in the same line as the pasted text convinces me that the middle mouse button is the culprit. In particular with worn mice it is all too easy to press the scroll wheel at the end of scrolling the text.

Do you think that this hypothesis matches your evidence?
Comment 8 Aryeh Weiss 2014-07-23 22:50:39 CDT 
Thank you for your reply. 
I think that the sticky-key or loose mouse button idea is not the explanation, because I have seen this happen on my mac, using a different mouse.
More important is that on my mac, I observed a spurious line appearing right after I opened the macro editor and loaded a script, before I did anything.
In that case, the spurious line was something that I had on the clipboard from some other program, and it was not related to Fiji. 
I reported this on 9-July-2014, but I did not capture it with a screencast, and it does not often happen this way on the OSX system.
Comment 9 Johannes Schindelin 2014-07-24 07:20:27 CDT 
> More important is that on my mac, I observed a spurious line appearing right after I opened the macro editor and loaded a script, before I did anything.

I have to admit that I am no longer using the script editor as often as I used to, but I never saw that happening...

How do you open the script editor? Personally, I start it by pressing the '[' key...
Comment 10 Aryeh Weiss 2014-07-24 10:17:52 CDT 
I usually use File>New>Script and then File>Open Recent... to get some script.
I use the script editor a lot. Much of my work involves designing some processing workflow, and then putting it into a script for whomever I am helping.

Today, I was working on the script to make spectral plots (which I posted today on the ImageJ list  in my question about that topic), and I saw that it was opening my image twice. Very strange. Then I saw that the run(`Bioformats...) line   which opened the file got inserted somewhere, without actually breaking the script. It has been on the clipboard, because I recorded it in order to get the arguments right.
Comment 11 Johannes Schindelin 2014-07-24 12:52:47 CDT 
Hmpf. We're now safely in the realm of crazy hypotheses: could you download and install a new Fiji, *not* follow any update site other than the default ones, and try with that setup's script editor? I have a hunch that the last possible explanation is one or more files from a 3rd-party update site. Unless somebody hacked into your computers and tries to unnerve you, of course ;-)
Comment 12 Aryeh Weiss 2014-07-25 07:35:33 CDT 
ok --I will remove what I do not need. I must have morphology, but that really should have nothing troublesome in it. I also need something in biovoxxel.

I will let you know after I have some experience with it.

Perhaps there is an event listener that pastes from the clipboard when it should not.